Alpha in fact can do both, remove Weapons and add Team color. Unfortunenately, its defined by the model, where the Alpha will add Team cololor and where it will just make things dissappear. Ingame, its easy to see where a model has the TC areas. Just cast Invisbility on them. The Team Color is often a layer under the actual model and its visible an a transparent model. So for example, the Crypt fiend has a TC area on the Abdomen, but nowhere else. This means, if you are editing the Alpha of the Skin, changing the abdomen will create TC areas, while changing it on toher parts will make things disappear.
Understood the prinziple?